We have just build a new server with S5520SC workstation board, Intel S5650WS chassis and Windows server 2008, I have one question though, how to enable wake up on lan settings from bios?

I have already enable both NIC eeproms, ACPI and BMC are also enabled, both "Allow ..." settings in power management in network device are also checked, wait for link set to forced, magic packed and direct are also set.

but i cant seem to able to wake up the server, i have other servers that wake up normally including an old one with S7520BD2 board ...

I did some test and didn't encounter any issue. There is no settings in BIOS, besides enabling onboard NIC ROM. Please download latest Network Driver, and install it by running the Windows_xxx_Install.bat file. After installing the driver, open the NIC in Device Manager, go to "Power Management" tab and check the "Wake on Magic Packet from power off state" box like below: